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Polysomes bypass a 50 nucleotide coding gap less efficiently than monosomes due to attenuation of an unstable 5’ mRNA stem loop stimulator and enhanced drop-off

ABSTRACT: Polysomes bypass a 50 nucleotide coding gap less efficiently than monosomes due to attenuation of an unstable 5’ mRNA stem loop stimulator and enhanced drop-off

PROVIDER: PRJNA609751 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11215525.fastq.gz	Fastqsanger.gz
	SRR11215526_1.fastq.gz	Fastqsanger.gz
	SRR11215526_2.fastq.gz	Fastqsanger.gz
	SRR11215527_1.fastq.gz	Fastqsanger.gz
	SRR11215527_2.fastq.gz	Fastqsanger.gz

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Polysomes bypass a 50 nucleotide coding gap less efficiently than monosomes due to attenuation of an unstable 5’ mRNA stem loop stimulator and enhanced drop-off

Project description:Ribosome profiling analysis of phage T4 infected E. coli yielded protected mRNA fragments within the normal size range derived from ribosomes stalled at the take-off codon. Ribosomes at this position also yielded some 53 nucleotide fragments, 16 longer. These were due to protection of the nucleotides that form the 5’ stem loop.

2020-06-01 | GSE146240 | GEO

Mouse cardiac tissue, polysomes and monosomes: Vehicle treated control vs. 25mg/kg DMNQ

Project description:Translational profiling of mouse cardiac tissue treated with 25mg/kg DMNQ in 10 ml/kg arachis oil over an acute time course (0.5-120 hours) compared to time matched control animals treated with 10ml/kg saline Two colour microarrays with time matched controls vs 25mg/kg DMNQ cardiac tissue. Before microarray analysis RNA separated on a sucrose density gradient into those mRNAs activitly undergoing translation (polysomes) and those not (monosomes) with control monosomes and treated monosomes on one set of arrays, and polysome control and polysome treated on another set of microarrays. The normalized Log2 of the monosomes was subtracted from the respective Log2 of the polysomes (on Series record). Time points studied were 0.5, 1, 2, 12, 24 and 120 hours following dosing, biological replicates n=3 independent animals at each time point, technical replicates (reverse labelling) n<1. One array printed onto two slides (A and B), one replicate per array.

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Mouse cardiac tissue, polysomes and monosomes: Vehicle treated control vs. 15mg/kg doxorubicin

Project description:Translational profiling of mouse cardiac tissue treated with 15mg/kg doxorubicin in 10 ml/kg saline over an acute time course (0.5-120 hours) compared to time matched control animals treated with 10ml/kg saline. Two colour microarrays with time matched controls vs 15mg/kg doxorubicin cardiac tissue. Before microarray analysis, RNA is separated on a sucrose density gradient into those mRNAs activity undergoing translation (polysomes) and those not (monosomes) with control monosomes and treated monosomes on one set of arrays, and polysome control and polysome treated on another set of microarrays. Thealized Log2 of the monosomes was subtracted from the respective Log2 of the polysomes (on Series record). Time points studied were 0.5, 1, 2, 12, 24 and 120 hours following dosing, biological replicates n=3 independent animals at each time point, technical replicates (reverse labelling) n<1. One array printed onto two slides (A and B), one replicate per array.

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RNA-seq of Trypanosoma brucei polysomes in response to ZC3H5 RNAi knockdown

Project description:ZC3H5 was knocked down in bloodstream form T.brucei by RNAi for 0h and 12h. WT bloodstream form cells were used as control. Polysome fractionation was performed, RNA was purified from each fraction and fractions were pooled the following: F=free fraction; M=monosomes; L=light polysomes; H=heavy polysomes. RNA was depleted and RNA-Seq was performed.

2019-06-28 | E-MTAB-8069 | biostudies-arrayexpress

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Polysomes Bypass a 50-Nucleotide Coding Gap Less Efficiently Than Monosomes Due to Attenuation of a 5' mRNA Stem-Loop and Enhanced Drop-off.

Project description:Efficient translational bypassing of a 50-nt non-coding gap in a phage T4 topoisomerase subunit gene (gp60) requires several recoding signals. Here we investigate the function of the mRNA stem-loop 5' of the take-off codon, as well as the importance of ribosome loading density on the mRNA for efficient bypassing. We show that polysomes are less efficient at mediating bypassing than monosomes, both in vitro and in vivo, due to their preventing formation of a stem-loop 5' of the take-off codon and allowing greater peptidyl-tRNA drop off. A ribosome profiling analysis of phage T4-infected Escherichia coli yielded protected mRNA fragments within the normal size range derived from ribosomes stalled at the take-off codon. However, ribosomes at this position also yielded some 53-nucleotide fragments, 16 longer. These were due to protection of the nucleotides that form the 5' stem-loop. NMR shows that the 5' stem-loop is highly dynamic. The importance of different nucleotides in the 5' stem-loop is revealed by mutagenesis studies. These data highlight the significance of the 5' stem-loop for the 50-nt bypassing and further enhance appreciation of relevance of the extent of ribosome loading for recoding.

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Project description:This SuperSeries is composed of the following subset Series: GSE17823: Mouse cardiac tissue, polysomes and monosomes: Vehicle treated control vs. 15mg/kg doxorubicin GSE17826: Mouse cardiac tissue: Vehicle treated control vs. 15mg/kg doxorubicin GSE17830: Mouse cardiac tissue, polysomes and monosomes: Vehicle treated control vs. 25mg/kg DMNQ GSE17915: Mouse cardiac tissue: Vehicle treated control vs. 25mg/kg DMNQ Refer to individual Series

2010-08-05 | E-GEOD-18459 | biostudies-arrayexpress

Ribosome profiling of polysomes from mouse brains

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